[Workers] Fix automatic configuration CLI docs

src/content/changelog/workers/2026-02-25-wrangler-autoconfig-ga.mdx

@@ -8,7 +8,7 @@ date: 2026-02-25
 
 You can now deploy any existing project to Cloudflare Workers — even without a Wrangler configuration file — and `wrangler deploy` will _just work_.
 
-Starting with Wrangler **4.68.0**, running [`wrangler deploy`](/workers/wrangler/commands/general/#deploy) [automatically configures your project](/workers/framework-guides/automatic-configuration/) by detecting your framework, installing required adapters, and deploying it to Cloudflare Workers.
+Starting with Wrangler **4.68.0**, running [`wrangler deploy`](/workers/wrangler/commands/workers/#deploy) [automatically configures your project](/workers/framework-guides/automatic-configuration/) by detecting your framework, installing required adapters, and deploying it to Cloudflare Workers.
 
 ### Using Wrangler locally
 
@@ -24,7 +24,7 @@ When you run `wrangler deploy` in a project without a configuration file, Wrangl
 4. Generates a `wrangler.jsonc` [configuration file](/workers/wrangler/configuration/)
 5. Deploys your project to Cloudflare Workers
 
-You can also use [`wrangler setup`](/workers/wrangler/commands/general/#setup) to configure without deploying, or pass [`--yes`](/workers/wrangler/commands/general/#deploy) to skip prompts.
+You can also use [`wrangler setup`](/workers/wrangler/commands/workers/#setup) to configure your project without deploying, and `wrangler setup --yes` to apply the detected configuration without confirmation.
 
 ### Using the Cloudflare dashboard
 

src/content/docs/workers/framework-guides/automatic-configuration.mdx

@@ -118,15 +118,15 @@ _routes.json
 
 ### Deploy with automatic configuration
 
-To deploy an existing project, run [`wrangler deploy`](/workers/wrangler/commands/general/#deploy) in your project directory:
+To deploy an existing project, run [`wrangler deploy`](/workers/wrangler/commands/workers/#deploy) in your project directory:
 
 <PackageManagers type="exec" pkg="wrangler" args="deploy" />
 
 Wrangler will detect your framework, show the configuration it will apply, and prompt you to confirm before making changes and deploying.
 
 ### Configure without deploying
 
-To configure your project without deploying, use [`wrangler setup`](/workers/wrangler/commands/general/#setup):
+To configure your project without deploying, use [`wrangler setup`](/workers/wrangler/commands/workers/#setup):
 
 <PackageManagers type="exec" pkg="wrangler" args="setup" />
 
@@ -140,13 +140,19 @@ To see what changes would be made without actually modifying any files:
 
 This outputs a summary of the configuration that would be generated.
 
-## Non-interactive mode
+## Skip configuration confirmation
 
-To skip the confirmation prompts, use the [`--yes` flag](/workers/wrangler/commands/general/#deploy):
+To apply the detected configuration without confirming it, pass `--yes` to [`wrangler setup`](/workers/wrangler/commands/workers/#setup):
 
-<PackageManagers type="exec" pkg="wrangler" args="deploy --yes" />
+<PackageManagers type="exec" pkg="wrangler" args="setup --yes" />
 
-This applies the configuration automatically using sensible defaults. This is useful in CI/CD environments or when you want to accept the detected settings without reviewing them.
+This is useful in CI/CD environments, or when you want to accept the detected settings without reviewing them.
+
+When setup finishes, Wrangler prints the command to deploy with. In a project with a `package.json`, use the generated `deploy` script:
+
+<PackageManagers type="run" args="deploy" />
+
+If Wrangler detected a build command, the generated script runs it before deploying. In a project without a `package.json`, run `wrangler deploy`.
 
 ## Importing a repository from the dashboard
 

src/content/docs/workers/wrangler/commands/workers.mdx

@@ -249,8 +249,6 @@ None of the options for this command are required. Also, many can be set in your
   - A tag for this Worker version. Matches the behavior of `wrangler versions upload --tag`.
 - `--message` <Type text="string" /> <MetaInfo text="optional" />
   - A descriptive message for this Worker version and deployment. Matches the behavior of `wrangler versions upload --message`. The message is also applied to the deployment.
-- `--yes` <Type text="boolean" /> <MetaInfo text="(default: false) optional" />
-  - Skip confirmation prompts and run [automatic project configuration](/workers/framework-guides/automatic-configuration/) non-interactively using detected settings. Only applicable when no Wrangler configuration file exists in your project.
 - `--temporary` <Type text="boolean" /> <MetaInfo text="optional" />
   - Deploy with a temporary preview account when no Cloudflare credentials are available. Requires Wrangler 4.102.0 or later. Wrangler prints a claim URL that lets you claim the deployment within 60 minutes. This is intended for AI agents and other first-time deployment flows. If Wrangler can already use OAuth, `CLOUDFLARE_API_TOKEN`, or a global API key, this flag returns an error. For more information, refer to [Claim deployments](/workers/platform/claim-deployments/).